data_3O3C
#
_model_server_result.job_id            WLGSsFGwKi0AjM71DACyeA 
_model_server_result.datetime_utc      '2024-11-05 01:19:00' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          3o3c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":901}' 
#
_entry.id    3O3C 
#
_exptl.entry_id    3O3C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.66 
_cell.angle_gamma         90 
_cell.entry_id            3O3C 
_cell.length_a            96.586 
_cell.length_b            167.209 
_cell.length_c            121.251 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3O3C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 G N N 
? 3 J N N 
? 3 O N N 
? 3 S N N 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N1 C2 UDP sing 360 n n 
N1 C6 UDP sing 361 n n 
N1 C1' UDP sing 362 n n 
C2 N3 UDP sing 363 n n 
C2 O2 UDP doub 364 n n 
N3 C4 UDP sing 365 n n 
N3 HN3 UDP sing 366 n n 
C4 C5 UDP sing 367 n n 
C4 O4 UDP doub 368 n n 
C5 C6 UDP doub 369 n n 
C5 H5 UDP sing 370 n n 
C6 H6 UDP sing 371 n n 
C1' C2' UDP sing 372 n n 
C1' O4' UDP sing 373 n n 
C1' H1' UDP sing 374 n n 
C2' O2' UDP sing 375 n n 
C2' C3' UDP sing 376 n n 
C2' H2' UDP sing 377 n n 
O2' HO2' UDP sing 378 n n 
C3' C4' UDP sing 379 n n 
C3' O3' UDP sing 380 n n 
C3' H3' UDP sing 381 n n 
C4' O4' UDP sing 382 n n 
C4' C5' UDP sing 383 n n 
C4' H4' UDP sing 384 n n 
O3' HO3' UDP sing 385 n n 
C5' O5' UDP sing 386 n n 
C5' "H5'1" UDP sing 387 n n 
C5' "H5'2" UDP sing 388 n n 
O5' PA UDP sing 389 n n 
PA O1A UDP doub 390 n n 
PA O2A UDP sing 391 n n 
PA O3A UDP sing 392 n n 
O2A HOA2 UDP sing 393 n n 
O3A PB UDP sing 394 n n 
PB O1B UDP doub 395 n n 
PB O2B UDP sing 396 n n 
PB O3B UDP sing 397 n n 
O2B HOB2 UDP sing 398 n n 
O3B HOB3 UDP sing 399 n n 
#
_atom_sites.entry_id                     3O3C 
_atom_sites.fract_transf_matrix[1][1]    0.010353 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002326 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005981 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.008453 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
E 2 SO4 A 1 801 801 SO4 SO4 . 
F 2 SO4 A 1 803 803 SO4 SO4 . 
G 3 UDP A 1 901 901 UDP UDP . 
H 2 SO4 B 1 801 801 SO4 SO4 . 
I 2 SO4 B 1 803 803 SO4 SO4 . 
J 3 UDP B 1 901 901 UDP UDP . 
K 2 SO4 B 1 802 802 SO4 SO4 . 
L 2 SO4 C 1 802 802 SO4 SO4 . 
M 2 SO4 C 1 801 801 SO4 SO4 . 
N 2 SO4 C 1 803 803 SO4 SO4 . 
O 3 UDP C 1 901 901 UDP UDP . 
P 2 SO4 D 1 802 802 SO4 SO4 . 
Q 2 SO4 D 1 801 801 SO4 SO4 . 
R 2 SO4 D 1 803 803 SO4 SO4 . 
S 3 UDP D 1 901 901 UDP UDP . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N1 UDP . . . J 3 47.367 24.842 26.331 1 109.17 ? N1 UDP 901 B 1 
HETATM 2 C C2 UDP . . . J 3 46.027 24.518 26.28 1 109.17 ? C2 UDP 901 B 1 
HETATM 3 N N3 UDP . . . J 3 45.443 24.076 25.11 1 109.17 ? N3 UDP 901 B 1 
HETATM 4 C C4 UDP . . . J 3 46.198 23.978 23.963 1 109.17 ? C4 UDP 901 B 1 
HETATM 5 C C5 UDP . . . J 3 47.543 24.33 24.029 1 109.17 ? C5 UDP 901 B 1 
HETATM 6 C C6 UDP . . . J 3 48.154 24.565 25.257 1 109.17 ? C6 UDP 901 B 1 
HETATM 7 O O2 UDP . . . J 3 45.345 24.605 27.295 1 109.17 ? O2 UDP 901 B 1 
HETATM 8 O O4 UDP . . . J 3 45.689 23.586 22.903 1 109.17 ? O4 UDP 901 B 1 
HETATM 9 C C1' UDP . . . J 3 47.96 25.346 27.591 1 109.17 ? C1' UDP 901 B 1 
HETATM 10 C C2' UDP . . . J 3 48.912 24.427 28.36 1 109.17 ? C2' UDP 901 B 1 
HETATM 11 O O2' UDP . . . J 3 48.354 23.95 29.575 1 109.17 ? O2' UDP 901 B 1 
HETATM 12 C C3' UDP . . . J 3 50.151 25.272 28.612 1 109.17 ? C3' UDP 901 B 1 
HETATM 13 C C4' UDP . . . J 3 49.827 26.637 28.06 1 109.17 ? C4' UDP 901 B 1 
HETATM 14 O O4' UDP . . . J 3 48.687 26.503 27.255 1 109.17 ? O4' UDP 901 B 1 
HETATM 15 O O3' UDP . . . J 3 50.385 25.438 29.988 1 109.17 ? O3' UDP 901 B 1 
HETATM 16 C C5' UDP . . . J 3 50.944 27.167 27.192 1 109.17 ? C5' UDP 901 B 1 
HETATM 17 O O5' UDP . . . J 3 51.845 27.961 27.923 1 109.17 ? O5' UDP 901 B 1 
HETATM 18 P PA UDP . . . J 3 52.353 29.356 27.32 1 109.17 ? PA UDP 901 B 1 
HETATM 19 O O1A UDP . . . J 3 53.093 29.077 26.072 1 109.17 ? O1A UDP 901 B 1 
HETATM 20 O O2A UDP . . . J 3 51.242 30.31 27.109 1 109.17 ? O2A UDP 901 B 1 
HETATM 21 O O3A UDP . . . J 3 53.336 29.924 28.458 1 109.17 ? O3A UDP 901 B 1 
HETATM 22 P PB UDP . . . J 3 54.681 29.163 28.901 1 109.17 ? PB UDP 901 B 1 
HETATM 23 O O1B UDP . . . J 3 54.73 29.048 30.371 1 109.17 ? O1B UDP 901 B 1 
HETATM 24 O O2B UDP . . . J 3 55.865 29.904 28.431 1 109.17 ? O2B UDP 901 B 1 
HETATM 25 O O3B UDP . . . J 3 54.693 27.816 28.309 1 109.17 ? O3B UDP 901 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#